------------------------------------------------------------ Pratt version 2.1, Sept. 1996 Written by Inge Jonassen, University of Bergen Norway email: inge@ii.uib.no For more information, see http://www.ii.uib.no/~inge/Pratt.html ------------------------------------------------------------ Please quote: I.Jonassen, J.F.Collins, D.G.Higgins. Protein Science 1995;4(8):1587-1595. ------------------------------------------------------------ Pratt version 2.1 Analysing 6 sequences from file 3_HYDROXYISOBUT_DH PATTERN CONSERVATION: CM: min Nr of Seqs to Match 6 C%: min Percentage Seqs to Match 100.0 PATTERN RESTRICTIONS : PP: pos in seq [off,complete,start] off PL: max Pattern Length 50 PN: max Nr of Pattern Symbols 50 PX: max Nr of consecutive x's 5 FN: max Nr of flexible spacers 2 FL: max Flexibility 2 FP: max Flex.Product 10 BI: Input Pattern Symbol File off BN: Nr of Pattern Symbols Initial Search 20 PATTERN SCORING: S: Scoring [info,mdl,tree,dist,ppv] info SEARCH PARAMETERS: G: Pattern Graph from [seq,al,query] seq E: Search Greediness 3 R: Pattern Refinement on RG: Generalise ambiguous symbols off OUTPUT: OF: Output Filename 3_HYDROXYISOBUT_DH.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: D3HI_HUMAN 11 D3HI_RABIT 35 D3HI_RAT 346 MMSB_PSEAE 298 YHAE_ECOLI 299 YIHU_ECOLI 298 Pratt run started at Thu Feb 6 18:25:34 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 12.5102 6( 6) F-x-G-L 2: 12.0102 6( 6) F-I-x(0,1)-G 3: 12.0102 9( 6) G-x(2,3)-G-L 4: 12.0102 6( 6) V-x(2,3)-G-L 5: 12.0102 9( 6) P-V-x(0,1)-G 6: 12.0102 7( 6) A-x(4)-V-x(3,4)-G 7: 11.5102 7( 6) G-x(0,1)-I-x(0,1)-L 8: 11.5102 11( 6) V-x(0,2)-G-x(2)-G 9: 11.5102 7( 6) K-x(2,3)-G-x(2,3)-L 10: 11.5102 8( 6) S-x(4)-G-x(1,3)-G 11: 11.5102 11( 6) S-x(4,5)-G-x(2,3)-G 12: 11.5102 7( 6) S-x(3,4)-G-x(1,2)-G 13: 11.5102 6( 6) A-x(0,1)-S-x(4,5)-G 14: 11.5102 6( 6) A-x-K-x(0,2)-V 15: 11.5102 7( 6) A-x(2)-T-x(1,3)-V 16: 11.5102 6( 6) A-x(3)-P-x(0,2)-V 17: 11.0102 7( 6) K-x(3,4)-G-x(2,4)-G 18: 11.0102 10( 6) S-x(2,3)-V-x(0,2)-G 19: 10.5102 7( 6) T-x(2,4)-G-x(1,3)-L 20: 10.5102 10( 6) K-x(0,2)-V-x(0,2)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 16.7645 6( 6) A-x(2)-T-x(1,3)-V-[AEG]-x(3)-[ALP] B 2: 15.9273 6( 6) S-x-[GNTV]-x-[AGTV]-G-x(1,3)-G C 3: 15.7968 6( 6) F-[IL]-G-L D 4: 15.1805 6( 6) F-I-x(0,1)-G-[GL] E 5: 14.6378 6( 6) A-x(3)-[PQS]-V-x(3,4)-G F 6: 14.6314 7( 6) P-V-x(0,1)-G-x(2)-[GPS] G 7: 14.1803 6( 6) S-x(2,3)-V-x(0,2)-G-x(3)-[AL] H 8: 14.1084 6( 6) A-x(0,1)-S-x(4,5)-G-x(2)-[GLV] I 9: 14.1076 6( 6) A-x-K-x(0,2)-V-x(4)-[ALV] J 10: 13.7494 11( 6) V-x(0,2)-G-x(2)-G-[AILV] K 11: 13.1720 8( 6) K-x(0,2)-V-x(0,2)-G-x-[ILV] L 12: 12.0102 9( 6) G-x(2,3)-G-L M 13: 12.0102 6( 6) V-x(2,3)-G-L N 14: 11.5102 7( 6) G-x(0,1)-I-x(0,1)-L O 15: 11.5102 7( 6) K-x(2,3)-G-x(2,3)-L P 16: 11.5102 11( 6) S-x(4,5)-G-x(2,3)-G Q 17: 11.5102 7( 6) S-x(3,4)-G-x(1,2)-G R 18: 11.5102 6( 6) A-x(3)-P-x(0,2)-V S 19: 11.0102 7( 6) K-x(3,4)-G-x(2,4)-G T 20: 10.5102 7( 6) T-x(2,4)-G-x(1,3)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 16.7645 6( 6) A-x(2)-T-x(1,3)-V-[AEG]-x(3)-[ALP] Occurences: 6(6) D3HI_HUMAN : 1- 11: AskTp--VGfigL D3HI_RABIT : 1- 11: AskTp--VGfigL gnmgn D3HI_RAT : 47- 57: csrsm AskTp--VGfigL gnmgn MMSB_PSEAE : 98- 110: dcsti ApeTarkVAeaaA akglt YHAE_ECOLI : 248- 260: kdlan AldTshgVGaqlP ltaav YIHU_ECOLI : 137- 149: tllll AggTaeqVEratP ilmam B 2: 15.9273 6( 6) S-x-[GNTV]-x-[AGTV]-G-x(1,3)-G Occurences: 6(6) D3HI_HUMAN : 2- 10: a SkTpVGfi-G l D3HI_RABIT : 2- 10: a SkTpVGfi-G lgnmg D3HI_RAT : 48- 56: srsma SkTpVGfi-G lgnmg MMSB_PSEAE : 122- 131: ldapv SgGvGGaraG tlsfi YHAE_ECOLI : 161- 169: kamag SvVhTGei-G agnvt YIHU_ECOLI : 207- 214: avkvm SgTaAGk--G hftts C 3: 15.7968 6( 6) F-[IL]-G-L Occurences: 6(6) D3HI_HUMAN : 8- 11: ktpvg FIGL D3HI_RABIT : 8- 11: ktpvg FIGL gnmgn D3HI_RAT : 54- 57: ktpvg FIGL gnmgn MMSB_PSEAE : 6- 9: mtdia FLGL gnmgg YHAE_ECOLI : 10- 13: tmkvg FIGL gimgk YIHU_ECOLI : 6- 9: maaia FIGL gqmgs D 4: 15.1805 6( 6) F-I-x(0,1)-G-[GL] Occurences: 6(6) D3HI_HUMAN : 8- 11: ktpvg FI-GL D3HI_RABIT : 8- 11: ktpvg FI-GL gnmgn D3HI_RAT : 54- 57: ktpvg FI-GL gnmgn MMSB_PSEAE : 135- 139: agtls FIvGG paegf YHAE_ECOLI : 10- 13: tmkvg FI-GL gimgk YIHU_ECOLI : 6- 9: maaia FI-GL gqmgs E 5: 14.6378 6( 6) A-x(3)-[PQS]-V-x(3,4)-G Occurences: 6(6) D3HI_HUMAN : 1- 10: AsktPVgfi-G l D3HI_RABIT : 1- 10: AsktPVgfi-G lgnmg D3HI_RAT : 47- 56: csrsm AsktPVgfi-G lgnmg MMSB_PSEAE : 145- 155: paegf ArarPVlenmG rnifh YHAE_ECOLI : 157- 166: ydlmk AmagSVvht-G eigag YIHU_ECOLI : 281- 291: rqdws AileQVrvsaG mtakv F 6: 14.6314 7( 6) P-V-x(0,1)-G-x(2)-[GPS] Occurences: 7(6) D3HI_HUMAN : 5- 10: askt PV-GfiG l D3HI_RABIT : 5- 10: askt PV-GfiG lgnmg D3HI_RAT : 51- 56: maskt PV-GfiG lgnmg D3HI_RAT : 168- 174: vfmda PVsGgvG aarsg MMSB_PSEAE : 120- 126: tllda PVsGgvG garag YHAE_ECOLI : 124- 130: dmlda PVsGgeP kaidg YIHU_ECOLI : 120- 125: smmdv PV-GrtS anait G 7: 14.1803 6( 6) S-x(2,3)-V-x(0,2)-G-x(3)-[AL] Occurences: 6(6) D3HI_HUMAN : 2- 11: a SktpV--GfigL D3HI_RABIT : 2- 11: a SktpV--GfigL gnmgn D3HI_RAT : 48- 57: srsma SktpV--GfigL gnmgn MMSB_PSEAE : 122- 130: ldapv Sgg-V--GgarA gtlsf YHAE_ECOLI : 138- 146: idgtl Svm-V--GgdkA ifdky YIHU_ECOLI : 115- 126: qakgf SmmdVpvGrtsA naitg H 8: 14.1084 6( 6) A-x(0,1)-S-x(4,5)-G-x(2)-[GLV] Occurences: 6(6) D3HI_HUMAN : 1- 10: A-Sktpv-GfiG l D3HI_RABIT : 1- 10: A-Sktpv-GfiG lgnmg D3HI_RAT : 47- 56: csrsm A-Sktpv-GfiG lgnmg MMSB_PSEAE : 231- 241: mpqap A-SngyagGfqV rlmnk YHAE_ECOLI : 159- 169: lmkam AgSvvht-GeiG agnvt YIHU_ECOLI : 17- 27: mgspm A-SnllqqGhqL rvfdv I 9: 14.1076 6( 6) A-x-K-x(0,2)-V-x(4)-[ALV] Occurences: 6(6) D3HI_HUMAN : 1- 11: AsKtpVgfigL D3HI_RABIT : 1- 11: AsKtpVgfigL gnmgn D3HI_RAT : 47- 57: csrsm AsKtpVgfigL gnmgn MMSB_PSEAE : 102- 110: iapet ArK--VaeaaA akglt YHAE_ECOLI : 196- 206: ealtl AtKagVnpdlV yqair YIHU_ECOLI : 202- 210: lpfdv AvK--VmsgtA agkgh J 10: 13.7494 11( 6) V-x(0,2)-G-x(2)-G-[AILV] Occurences: 11(6) D3HI_HUMAN : 6- 11: asktp V--GfiGL D3HI_RABIT : 6- 11: asktp V--GfiGL gnmgn D3HI_RAT : 52- 57: asktp V--GfiGL gnmgn D3HI_RAT : 122- 129: mnsie VysGanGI lkkvk D3HI_RAT : 169- 175: fmdap Vs-GgvGA arsgn MMSB_PSEAE : 41- 48: avlgl VeqGaqGA dsalq MMSB_PSEAE : 121- 128: lldap VsgGvgGA ragtl YHAE_ECOLI : 8- 13: dmtmk V--GfiGL gimgk YHAE_ECOLI : 78- 85: phvke ValGenGI iegak YHAE_ECOLI : 163- 170: magsv VhtGeiGA gnvtk YIHU_ECOLI : 74- 81: dlvrn VlfGenGV cegls K 11: 13.1720 8( 6) K-x(0,2)-V-x(0,2)-G-x-[ILV] Occurences: 8(6) D3HI_HUMAN : 3- 9: as KtpV--GfI gl D3HI_RABIT : 3- 9: as KtpV--GfI glgnm D3HI_RAT : 49- 55: rsmas KtpV--GfI glgnm D3HI_RAT : 131- 138: angil Kk-VkkGsL lidss D3HI_RAT : 132- 138: ngilk K--VkkGsL lidss MMSB_PSEAE : 35- 41: fdlqp Ka-Vl-GlV eqgaq YHAE_ECOLI : 7- 11: idmtm K--V--GfI glgim YIHU_ECOLI : 223- 229: tswpn K--VlsGdL spafm L 12: 12.0102 9( 6) G-x(2,3)-G-L Occurences: 9(6) D3HI_HUMAN : 7- 11: sktpv Gfi-GL D3HI_RABIT : 7- 11: sktpv Gfi-GL gnmgn D3HI_RAT : 20- 25: pwgsg GhasGL rywsg D3HI_RAT : 53- 57: sktpv Gfi-GL gnmgn D3HI_RAT : 240- 245: eamnl GirsGL dpkll MMSB_PSEAE : 77- 81: eslyl Gdd-GL larva MMSB_PSEAE : 192- 197: ealal GvknGL dpavl YHAE_ECOLI : 9- 13: mtmkv Gfi-GL gimgk YIHU_ECOLI : 80- 85: lfgen GvceGL stdal M 13: 12.0102 6( 6) V-x(2,3)-G-L Occurences: 6(6) D3HI_HUMAN : 6- 11: asktp VgfiGL D3HI_RABIT : 6- 11: asktp VgfiGL gnmgn D3HI_RAT : 52- 57: asktp VgfiGL gnmgn MMSB_PSEAE : 193- 197: alalg Vkn-GL dpavl YHAE_ECOLI : 8- 13: dmtmk VgfiGL gimgk YIHU_ECOLI : 81- 85: fgeng Vce-GL stdal N 14: 11.5102 7( 6) G-x(0,1)-I-x(0,1)-L Occurences: 7(6) D3HI_HUMAN : 7- 11: sktpv GfIgL D3HI_RABIT : 7- 11: sktpv GfIgL gnmgn D3HI_RAT : 53- 57: sktpv GfIgL gnmgn D3HI_RAT : 128- 130: ysgan G-I-L kkvkk MMSB_PSEAE : 179- 181: nnmll G-I-L magta YHAE_ECOLI : 9- 13: mtmkv GfIgL gimgk YIHU_ECOLI : 243- 246: ahkdl G-IaL dvanq O 15: 11.5102 7( 6) K-x(2,3)-G-x(2,3)-L Occurences: 7(6) D3HI_HUMAN : 3- 11: as KtpvGfigL D3HI_RABIT : 3- 11: as KtpvGfigL gnmgn D3HI_RAT : 49- 57: rsmas KtpvGfigL gnmgn D3HI_RAT : 132- 139: ngilk KvkkGsl-L idsst MMSB_PSEAE : 246- 252: vrlmn Kdl-Gla-L anaqa YHAE_ECOLI : 114- 121: iseal Kak-GidmL dapvs YIHU_ECOLI : 240- 246: idlah Kdl-Gia-L dvanq P 16: 11.5102 11( 6) S-x(4,5)-G-x(2,3)-G Occurences: 11(6) D3HI_HUMAN : 2- 10: a Sktpv-Gfi-G l D3HI_RABIT : 2- 10: a Sktpv-Gfi-G lgnmg D3HI_RAT : 48- 56: srsma Sktpv-Gfi-G lgnmg D3HI_RAT : 119- 128: pssmn SievysGan-G ilkkv D3HI_RAT : 204- 213: lgcmg SnvlycGav-G sgqsa D3HI_RAT : 279- 288: mdgvp SsnnyqGgf-G ttlma D3HI_RAT : 280- 288: dgvps Snnyq-Ggf-G ttlma MMSB_PSEAE : 122- 131: ldapv Sggvg-GaraG tlsfi MMSB_PSEAE : 134- 143: ragtl Sfivg-GpaeG farar YHAE_ECOLI : 161- 169: kamag Svvht-Gei-G agnvt YIHU_ECOLI : 156- 165: lmamg SelinaGgp-G mgirv Q 17: 11.5102 7( 6) S-x(3,4)-G-x(1,2)-G Occurences: 7(6) D3HI_HUMAN : 2- 10: a SktpvGfiG l D3HI_RABIT : 2- 10: a SktpvGfiG lgnmg D3HI_RAT : 48- 56: srsma SktpvGfiG lgnmg D3HI_RAT : 280- 288: dgvps SnnyqGgfG ttlma MMSB_PSEAE : 73- 80: gqhve Slyl-GddG llarv YHAE_ECOLI : 161- 169: kamag SvvhtGeiG agnvt YIHU_ECOLI : 207- 214: avkvm SgtaaGk-G hftts R 18: 11.5102 6( 6) A-x(3)-P-x(0,2)-V Occurences: 6(6) D3HI_HUMAN : 1- 6: AsktP--V gfigl D3HI_RABIT : 1- 6: AsktP--V gfigl D3HI_RAT : 47- 52: csrsm AsktP--V gfigl MMSB_PSEAE : 145- 150: paegf ArarP--V lenmg YHAE_ECOLI : 199- 206: tlatk AgvnPdlV yqair YIHU_ECOLI : 194- 201: avlce AlnlPfdV avkvm S 19: 11.0102 7( 6) K-x(3,4)-G-x(2,4)-G Occurences: 7(6) D3HI_HUMAN : 3- 10: as Ktpv-Gfi--G l D3HI_RABIT : 3- 10: as Ktpv-Gfi--G lgnmg D3HI_RABIT : 3- 12: as Ktpv-GfiglG nmgnp D3HI_RAT : 49- 56: rsmas Ktpv-Gfi--G lgnmg D3HI_RAT : 49- 58: rsmas Ktpv-GfiglG nmgnp MMSB_PSEAE : 35- 44: fdlqp Kavl-GlveqG aqgad YHAE_ECOLI : 7- 17: idmtm KvgfiGlgimG kpmsk YHAE_ECOLI : 76- 84: nsphv KevalGen--G iiega YIHU_ECOLI : 204- 212: fdvav Kvms-Gtaa-G kghft T 20: 10.5102 7( 6) T-x(2,4)-G-x(1,3)-L Occurences: 7(6) D3HI_HUMAN : 4- 11: ask Tpv--GfigL D3HI_RABIT : 4- 11: ask Tpv--GfigL gnmgn D3HI_RAT : 50- 57: smask Tpv--GfigL gnmgn MMSB_PSEAE : 262- 267: avqas Tpl--Ga--L arnlf YHAE_ECOLI : 5- 13: midm Tmkv-GfigL gimgk YHAE_ECOLI : 251- 259: anald TshgvGaq-L pltaa YIHU_ECOLI : 63- 70: aefii TmlpnGd--L vrnvl Number of patterns evaluated by Pratt:148 Total running time: 0 seconds